fulltext.study @t Gmail

Assembly of repetitive regions using next-generation sequencing data

Paper ID Volume ID Publish Year Pages File Format Full-Text
5183 347 2015 8 PDF Available
Title
Assembly of repetitive regions using next-generation sequencing data
Abstract

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read.I propose a new algorithm for a DNA assembly which uses the relative frequency of reads to properly reconstruct repetitive sequences. The mathematical model for error-free input data shows the upper limits of accuracy of the results as a function of read coverage. For high coverage, the estimation error depends linearly on repetitive sequence length and inversely proportional to the sequencing coverage. The model depicts, the smaller de Bruijn graph dimensions, the more accurate assembly of long repetitive regions.The algorithm requires high read depth, provided by the next-generation sequencers and could use the existing data. The tests on errorless reads, generated in silico from several model genomes, pointed the properly reconstructed repetitive sequences, where existing assemblers fail.The C++ sources, the Python scripts and the additional data are available at http://dnaasm.sourceforge.net.

Keywords
Genome assembler; Repetitive sequences; Mathematical model; Next generation sequencing; de Bruijn graph parameters
First Page Preview
Assembly of repetitive regions using next-generation sequencing data
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us
Publisher
Database: Elsevier - ScienceDirect
Journal: Biocybernetics and Biomedical Engineering - Volume 35, Issue 4, 2015, Pages 276–283
Authors
,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us